Pre-visualization of the normalized count data before any differential analysis

Load

Libraries and functions

Warning message in is.na(x[[i]]):
“is.na() applied to non-(list or vector) of type 'environment'”Warning message in rsqlite_fetch(res@ptr, n = n):
“Don't need to call dbFetch() for statements, only for queries”
==========================================================================
*
*  Package WGCNA 1.63 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=4
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=4
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


Allowing multi-threading with up to 4 threads.
[1] "preparing gene to GO mapping data..."
[1] "preparing IC data..."
[1] "preparing gene to GO mapping data..."
[1] "preparing IC data..."
[1] "preparing gene to GO mapping data..."
[1] "preparing IC data..."

Data

GF_104w_F_1_2GF_104w_F_2_2GF_104w_F_3_2GF_104w_M_1_2GF_104w_M_2_2GF_52w_M_1_2GF_52w_M_2_2GF_52w_M_3_2GF_52w_M_4_2GF_8w_M_1_2⋯SPF_8w_F_4_2SPF_8w_F_5_2GF_8w_F_1_2GF_8w_F_2_2GF_8w_F_3_2GF_8w_F_4_2GF_8w_F_5_2GF_104w_M_3_2GF_104w_M_5_2GF_104w_M_4_2
0610005C13Rik 0.00000 0.00000 0.00000 1.747854 1.244311 0.8338695 4.892544 5.547012 7.158344 8.384882 ⋯ 2.57208 0.00000 18.04370 0.00000 2.001891 5.212621 0.00000 1.243886 1.039189 1.495931
0610007P14Rik 857.59757 740.81613 899.06639 875.674692 981.138840 503.6571924525.459208 509.215656 730.866890 597.722277 ⋯ 897.65596 947.91171 888.38701 674.46562 605.571925 586.941079 799.60448 490.090915 592.337898 741.981645
0610009B22Rik1008.62104 1155.42062 1166.35639 1210.388671 1539.834260 1028.9949924867.937277 1006.227887 869.022923 939.106744 ⋯ 1280.89590 1431.97437 1028.49105 1009.00917 1129.066334 949.739473 1080.92333 685.380950 802.254135 780.875844
0610009L18Rik 27.86743 35.77805 17.99933 20.100317 37.951471 31.6870419 26.419737 22.188046 4.295006 61.089852 ⋯ 101.59716 71.27956 47.76274 19.36265 11.010399 44.828537 24.07684 24.877711 22.862164 38.894199
0610009O20Rik 214.84887 275.70146 262.79017 223.725271 268.771071 296.8575505346.392104 391.619012 306.377109 356.956390 ⋯ 225.05701 182.98632 229.26116 157.05260 268.253349 301.289471 266.11243 334.605219 364.755442 393.429783
0610010B08Rik 0.00000 0.00000 0.00000 0.000000 0.000000 0.0000000 0.000000 0.000000 0.000000 0.000000 ⋯ 0.00000 0.00000 0.00000 0.00000 0.000000 0.000000 0.00000 0.000000 0.000000 0.000000

Sample clustering

With all genes

Without X/Y genes

PCA

Gene co-expression network analysis

Build network

  1. 24421
  2. 63
  1. 11170
  2. 63
pickSoftThreshold: will use block size 4005.
 pickSoftThreshold: calculating connectivity for given powers...
   ..working on genes 1 through 4005 of 11170
   ..working on genes 4006 through 8010 of 11170
   ..working on genes 8011 through 11170 of 11170
   Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k.  max.k.
1      1   0.0868  0.882          0.888 1080.000  1.09e+03 1690.00
2      2   0.2860 -1.170          0.863  336.000  3.22e+02  799.00
3      3   0.5750 -1.720          0.923  133.000  1.16e+02  460.00
4      4   0.6710 -2.020          0.935   61.500  4.70e+01  296.00
5      5   0.7370 -2.100          0.954   31.700  2.09e+01  205.00
6      6   0.7430 -2.220          0.956   17.700  9.85e+00  148.00
7      7   0.7790 -2.190          0.968   10.600  4.92e+00  111.00
8      8   0.7990 -2.150          0.974    6.640  2.53e+00   85.60
9      9   0.8190 -2.120          0.978    4.350  1.35e+00   67.20
10    10   0.8340 -2.050          0.982    2.950  7.41e-01   53.70
11    12   0.8560 -1.950          0.986    1.470  2.38e-01   35.60
12    14   0.8730 -1.870          0.986    0.802  8.27e-02   24.50
13    16   0.8820 -1.800          0.979    0.468  3.12e-02   17.30
14    18   0.9180 -1.690          0.985    0.288  1.19e-02   12.50
15    20   0.9420 -1.600          0.988    0.185  4.79e-03    9.16
PowerSFT.R.sqslopetruncated.R.sqmean.k.median.k.max.k.
1 0.08682157 0.8820601 0.8877917 1081.10685651.089741e+031686.156755
2 0.28622457 -1.1729565 0.8631891 336.34618123.222064e+02 798.575992
3 0.57483023 -1.7238558 0.9230250 133.07665391.155664e+02 460.255658
4 0.67059084 -2.0210959 0.9346949 61.47490484.700680e+01 296.282031
5 0.73662969 -2.1024598 0.9538173 31.69242962.089565e+01 204.558497
6 0.74338186 -2.2197752 0.9564366 17.73736759.852889e+00 148.173791
7 0.77934389 -2.1914854 0.9684850 10.58156464.915240e+00 111.129137
8 0.79898550 -2.1545864 0.9744351 6.64315632.525501e+00 85.561574
9 0.81862291 -2.1163663 0.9783691 4.34824601.346482e+00 67.234901
10 0.83443100 -2.0512651 0.9824172 2.94666847.411700e-01 53.700873
12 0.85590807 -1.9520372 0.9863926 1.47149132.384285e-01 35.566779
14 0.87303836 -1.8717587 0.9862762 0.80211588.270069e-02 24.454629
16 0.88236278 -1.7975866 0.9794021 0.46773933.116421e-02 17.284522
18 0.91753298 -1.6901870 0.9847788 0.28775871.192253e-02 12.479439
20 0.94216559 -1.6019139 0.9880597 0.18492434.786690e-03 9.164832
Powermean.k.
9 9 4.3482460
1010 2.9466684
1112 1.4714913
1214 0.8021158
1316 0.4677393
1418 0.2877587
1520 0.1849243

Parameters for network construction

 Calculating module eigengenes block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
 ....pre-clustering genes to determine blocks..
   Projective K-means:
   ..k-means clustering..
   ..merging smaller clusters...
Block sizes:
gBlocks
   1    2 
7606 3564 
 ..Working on block 1 .
    TOM calculation: adjacency..
    ..will use 4 parallel threads.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
   ..saving TOM for block 1 into file norm_genes_TOM-block.1.RData
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 2 genes from module 1 because their KME is too low.
     ..removing 1 genes from module 6 because their KME is too low.
 ..Working on block 2 .
    TOM calculation: adjacency..
    ..will use 4 parallel threads.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
   ..saving TOM for block 2 into file norm_genes_TOM-block.2.RData
 ....clustering..
 ....detecting modules..
 ....calculating module eigengenes..
 ....checking kME in modules..
     ..removing 2 genes from module 2 because their KME is too low.
     ..removing 3 genes from module 4 because their KME is too low.
 ..merging modules that are too close..
     mergeCloseModules: Merging modules whose distance is less than 0.35
       Calculating new MEs...

 ME0  ME1  ME2  ME3  ME4  ME5  ME6  ME7  ME8  ME9 ME10 ME11 
6174 1565  806  781  612  374  324  179  162   80   73   40
11
  • 11 modules with between 40 and 1565 genes
  • 6174 genes not assigned to a module
4996
4996
0
'grey'
1
'turquoise'
2
'blue'
3
'brown'
4
'yellow'
5
'green'
6
'red'
7
'black'
8
'pink'
9
'magenta'
10
'purple'
11
'greenyellow'

Network visualization

TOM calculation: adjacency..
..will use 4 parallel threads.
 Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
0610007P14Rik0610009B22Rik0610009O20Rik0610010K14RikMettl260610030E20Rik0610037L13RikFmc11110004F10RikCard19⋯Zswim6Zswim7Zswim8ZufspZxdaZyg11bZyxZzef1Zzz3Hikeshi
0610007P14Rik1100000000⋯0010000000
0610009B22Rik1100000000⋯0000000001
0610009O20Rik0010000000⋯0010000000
0610010K14Rik0001000101⋯0100010001
Mettl260000100001⋯0000000000
0610030E20Rik0000011000⋯1011000110
0610007P14Rik
'4'
0610009B22Rik
'5'
0610009O20Rik
'1'
0610010K14Rik
'4'
Mettl26
'4'
0610030E20Rik
'1'
4
'yellow'
5
'green'
1
'turquoise'
4
'yellow'
4
'yellow'
1
'turquoise'

Module analysis

1565 
[1] 1

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
17799 GO:0090304            6.732271e-37                        1        566
5756  GO:0016070            1.348307e-32                        1        511
3020  GO:0006139            3.396777e-29                        1        581
12953 GO:0046483            6.883528e-28                        1        584
4834  GO:0010467            1.653568e-27                        1        556
3420  GO:0006725            1.060674e-26                        1        585
      numInCat                                             term ontology
17799     4325                   nucleic acid metabolic process       BP
5756      3872                            RNA metabolic process       BP
3020      4848 nucleobase-containing compound metabolic process       BP
12953     4947                    heterocycle metabolic process       BP
4834      4726                                  gene expression       BP
3420      5011     cellular aromatic compound metabolic process       BP
[1] 2

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
16368 GO:0070647            3.091339e-13                        1         80
5997  GO:0016567            1.909439e-12                        1         67
14460 GO:0051603            2.417010e-12                        1         67
8648  GO:0032446            4.636519e-12                        1         69
11979 GO:0044257            2.173275e-11                        1         67
7417  GO:0030163            2.493776e-11                        1         75
      numInCat                                                         term
16368      694 protein modification by small protein conjugation or removal
5997       541                                       protein ubiquitination
14460      590   proteolysis involved in cellular protein catabolic process
8648       582            protein modification by small protein conjugation
11979      622                           cellular protein catabolic process
7417       745                                    protein catabolic process
      ontology
16368       BP
5997        BP
14460       BP
8648        BP
11979       BP
7417        BP
[1] 3

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
16937 GO:0071704            2.743919e-23                        1        490
11965 GO:0044238            4.928763e-23                        1        470
3974  GO:0008152            3.120018e-22                        1        502
11964 GO:0044237            5.312527e-22                        1        466
4377  GO:0009056            2.322063e-20                        1        139
12158 GO:0044710            5.886847e-20                        1        232
      numInCat                                term ontology
16937     9446 organic substance metabolic process       BP
11965     8887           primary metabolic process       BP
3974      9868                   metabolic process       BP
11964     8866          cellular metabolic process       BP
4377      1611                   catabolic process       BP
12158     3454   single-organism metabolic process       BP
[1] 4

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
9705  GO:0034641            4.807047e-33                        1        250
11964 GO:0044237            1.535082e-32                        1        339
3974  GO:0008152            4.655645e-32                        1        370
17005 GO:0071840            1.196809e-30                        1        233
3590  GO:0007005            2.174423e-30                        1         78
3465  GO:0006807            7.690920e-30                        1        252
      numInCat                                          term ontology
9705      5508  cellular nitrogen compound metabolic process       BP
11964     8866                    cellular metabolic process       BP
3974      9868                             metabolic process       BP
17005     5620 cellular component organization or biogenesis       BP
3590       621                    mitochondrion organization       BP
3465      5831           nitrogen compound metabolic process       BP
[1] 5

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
11972 GO:0044248            1.349996e-10                        1         58
12359 GO:0045184            3.791994e-09                        1         68
11984 GO:0044265            4.130686e-09                        1         40
4378  GO:0009057            7.501194e-09                        1         45
4377  GO:0009056            1.754315e-08                        1         61
18903 GO:1901575            2.194517e-08                        1         59
      numInCat                                     term ontology
11972     1304               cellular catabolic process       BP
12359     1809    establishment of protein localization       BP
11984      793 cellular macromolecule catabolic process       BP
4378       980          macromolecule catabolic process       BP
4377      1611                        catabolic process       BP
18903     1540      organic substance catabolic process       BP
[1] 6

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
3557  GO:0006952            7.626613e-19                        1         66
3560  GO:0006955            2.189496e-18                        1         60
1052  GO:0002376            1.020968e-17                        1         87
10116 GO:0035456            1.376979e-16                        1         15
4620  GO:0009605            5.104588e-15                        1         76
3556  GO:0006950            1.960846e-14                        1        103
      numInCat                          term ontology
3557      1323              defense response       BP
3560      1110               immune response       BP
1052      2158         immune system process       BP
10116       46   response to interferon-beta       BP
4620      1907 response to external stimulus       BP
3556      3099            response to stress       BP
[1] 7

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
12158 GO:0044710            1.973405e-07                0.9999999         58
13556 GO:0048518            2.788819e-07                0.9999999         74
13560 GO:0048522            1.398066e-06                0.9999994         67
11965 GO:0044238            1.443017e-06                0.9999993        108
5242  GO:0014067            2.674909e-06                1.0000000          4
16937 GO:0071704            3.986056e-06                0.9999981        111
      numInCat                                                           term
12158     3454                              single-organism metabolic process
13556     4974                      positive regulation of biological process
13560     4482                        positive regulation of cellular process
11965     8887                                      primary metabolic process
5242        12 negative regulation of phosphatidylinositol 3-kinase signaling
16937     9446                            organic substance metabolic process
      ontology
12158       BP
13556       BP
13560       BP
11965       BP
5242        BP
16937       BP
[1] 8

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
3468  GO:0006810            2.240896e-05                0.9999895         57
14240 GO:0051234            3.402958e-05                0.9999837         58
3458  GO:0006790            4.123608e-05                0.9999931         10
      numInCat                              term ontology
3468      4082                         transport       BP
14240     4231     establishment of localization       BP
3458       262 sulfur compound metabolic process       BP
[1] 9

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)
[1] 10

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

        category over_represented_pvalue under_represented_pvalue numDEInCat
15    GO:0000028                       0                        1          8
936   GO:0002181                       0                        1          9
3177  GO:0006412                       0                        1         41
3251  GO:0006518                       0                        1         41
10964 GO:0042255                       0                        1          9
10976 GO:0042274                       0                        1         12
      numInCat                               term ontology
15          19   ribosomal small subunit assembly       BP
936         49            cytoplasmic translation       BP
3177       597                        translation       BP
3251       738          peptide metabolic process       BP
10964       52                  ribosome assembly       BP
10976       66 ribosomal small subunit biogenesis       BP
[1] 11

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations...
For 2918 genes, we could not find any categories. These genes will be excluded.
To force their use, please run with use_genes_without_cat=TRUE (see documentation).
This was the default behavior for version 1.15.1 and earlier.
Calculating the p-values...
'select()' returned 1:1 mapping between keys and columns

[1] category                 over_represented_pvalue  under_represented_pvalue
[4] numDEInCat               numInCat                 term                    
[7] ontology                
<0 rows> (or 0-length row.names)

[1] "1: 40 - 2.55591054313099%"
[1] "2: 41 - 5.08684863523573%"
[1] "3: 17 - 2.17669654289373%"
[1] "4: 15 - 2.45098039215686%"
[1] "5: 14 - 3.74331550802139%"
[1] "6: 7 - 2.16049382716049%"
[1] "7: 3 - 1.67597765363128%"
[1] "8: 8 - 4.93827160493827%"
[1] "9: 2 - 2.5%"
[1] "10: 3 - 4.10958904109589%"
[1] "11: 0 - 0%"

Relation between modules and samples

Functional gene network

  1. 6537
  2. 24421
Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“EOF within quoted string”Warning message in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
“number of items read is not a multiple of the number of columns”
  1. 1341
  2. 182
  3. 1513

Tree with all GOs at "../results/dge/global_GO_network.png"

  1. FALSE
  2. FALSE
  3. FALSE
6537
6207
5643
$`0610009O20RIK`
  1. 'GO:0006508'
  2. 'GO:0006915'
  3. 'GO:0007154'
  4. 'GO:0007165'
  5. 'GO:0007166'
  6. 'GO:0008152'
  7. 'GO:0008219'
  8. 'GO:0009987'
  9. 'GO:0010941'
  10. 'GO:0012501'
  11. 'GO:0019222'
  12. 'GO:0019538'
  13. 'GO:0023052'
  14. 'GO:0042981'
  15. 'GO:0043067'
  16. 'GO:0043170'
  17. 'GO:0043281'
  18. 'GO:0044238'
  19. 'GO:0044699'
  20. 'GO:0044700'
  21. 'GO:0044763'
  22. 'GO:0050789'
  23. 'GO:0050790'
  24. 'GO:0050794'
  25. 'GO:0050896'
  26. 'GO:0051246'
  27. 'GO:0051716'
  28. 'GO:0060255'
  29. 'GO:0065007'
  30. 'GO:0071704'
  31. 'GO:0080090'
  32. 'GO:0097190'
  33. 'GO:0005622'
  34. 'GO:0005623'
  35. 'GO:0005737'
  36. 'GO:0043226'
  37. 'GO:0043227'
  38. 'GO:0043229'
  39. 'GO:0043231'
  40. 'GO:0044424'
  41. 'GO:0044464'
$FMC1
  1. 'GO:0008152'
  2. 'GO:0008283'
  3. 'GO:0009987'
  4. 'GO:0019222'
  5. 'GO:0042127'
  6. 'GO:0044238'
  7. 'GO:0044699'
  8. 'GO:0048519'
  9. 'GO:0050789'
  10. 'GO:0050794'
  11. 'GO:0061469'
  12. 'GO:0065007'
  13. 'GO:0071704'
  14. 'GO:0080090'
  15. 'GO:0005622'
  16. 'GO:0005623'
  17. 'GO:0005737'
  18. 'GO:0043226'
  19. 'GO:0043227'
  20. 'GO:0043229'
  21. 'GO:0043231'
  22. 'GO:0044424'
  23. 'GO:0044464'
$`1190002N15RIK`
  1. 'GO:0007154'
  2. 'GO:0007165'
  3. 'GO:0007275'
  4. 'GO:0008283'
  5. 'GO:0009966'
  6. 'GO:0009987'
  7. 'GO:0010646'
  8. 'GO:0023051'
  9. 'GO:0023052'
  10. 'GO:0032501'
  11. 'GO:0032502'
  12. 'GO:0035556'
  13. 'GO:0044699'
  14. 'GO:0044700'
  15. 'GO:0044707'
  16. 'GO:0044763'
  17. 'GO:0044767'
  18. 'GO:0048513'
  19. 'GO:0048583'
  20. 'GO:0048731'
  21. 'GO:0048856'
  22. 'GO:0050789'
  23. 'GO:0050794'
  24. 'GO:0050896'
  25. 'GO:0051179'
  26. 'GO:0051716'
  27. 'GO:0065007'
  28. 'GO:1902531'
  29. 'GO:0005576'
  30. 'GO:0005615'
  31. 'GO:0005622'
  32. 'GO:0005623'
  33. 'GO:0005737'
  34. 'GO:0016020'
  35. 'GO:0031982'
  36. 'GO:0031988'
  37. 'GO:0032991'
  38. 'GO:0043226'
  39. 'GO:0043227'
  40. 'GO:0043229'
  41. 'GO:0043231'
  42. 'GO:0044421'
  43. 'GO:0044422'
  44. 'GO:0044424'
  45. 'GO:0044425'
  46. 'GO:0044446'
  47. 'GO:0044464'
$`1600002K03RIK`
  1. 'GO:0005576'
  2. 'GO:0005622'
  3. 'GO:0005623'
  4. 'GO:0005737'
  5. 'GO:0016020'
  6. 'GO:0031224'
  7. 'GO:0044424'
  8. 'GO:0044425'
  9. 'GO:0044464'
$`1600014C10RIK`
  1. 'GO:0005622'
  2. 'GO:0005623'
  3. 'GO:0005737'
  4. 'GO:0016020'
  5. 'GO:0031224'
  6. 'GO:0043226'
  7. 'GO:0043227'
  8. 'GO:0043229'
  9. 'GO:0043231'
  10. 'GO:0044424'
  11. 'GO:0044425'
  12. 'GO:0044464'
$`1700029J07RIK`
  1. 'GO:0005622'
  2. 'GO:0005623'
  3. 'GO:0005737'
  4. 'GO:0005856'
  5. 'GO:0015630'
  6. 'GO:0043226'
  7. 'GO:0043228'
  8. 'GO:0043229'
  9. 'GO:0043232'
  10. 'GO:0044422'
  11. 'GO:0044424'
  12. 'GO:0044430'
  13. 'GO:0044446'
  14. 'GO:0044464'

Median of gene counts in the modules over ages